Starting in the 2360s, he worked on the controversial Distant Origin Theory, which contended that contrary to doctrine, the Voth did not originate in the space they occupied, but evolved in some other part of the galaxy and traveled there later. To protect him in this dangerous persuit, he relied on a network of supporters, in the Circle of Archeology and on the Fourth Colony. Shortly before his trial, he circulated a study criticizing what he called "resistance to truth", which the Voth Ministry of Elders viewed as disputing official doctrine.

In 2373, Gegen had a breakthrough when he discovered the bones of a humanoid, CrewmanHogan, whose genetic makeup bore compelling similarities to his own, on Hanon IV. He was able to determine that the bones came from the shipUSS Voyager, which then he tracked down. He and a trusted assistant, Tova Veer to which he was a mentor, boarded under cloak and studied the crew until they were discovered. Veer was captured while Gegen abducted Chakotay, who had been knocked out by Veer. Chakotay helped Gegen find more evidence for his theory. Chakotay went with Gegen back to the Voth city ship to present his evidence.

The Voth Ministry of Elders did not look kindly upon the new evidence, and charged the professor with heresy. In this trial it became clear that Gegen had come to believe that the ministry did not care about the truth, and was only interested in perpetuating a myth that kept them in power.

MinisterOdala tried to force Gegen to retract his claims. Veer was threatened, and he recanted and denounced Professor Gegen. Gegen refused to retract his theories until Odala threatened to imprison the crew of Voyager for life and destroy the ship. Having been unable to meet up with his supporters on the Fourth Colony, Gegen was too weak and had to submit. He was relieved of duty and reassigned to a job as a metallurgical scientist, a career in which he felt he would be undistinguished. However, as Chakotay departed Gegen's ship, he gave his friend a globe of Earth, and Gegen expressed his wish that, someday, all Voth would call Earth "home".